While researchers said they didn't know if long-term bottle-feeding was directly to blame, they said their findings suggested that weaning babies around their first birthday could help fight weight gain.
"Prolonged bottle use was associated with obesity at 5.5 years of age," wrote study leader Rachel Gooze.
"Avoiding this behaviour may help prevent early childhood obesity."
Paediatricians already advise parents to wean children from the bottle to toddler-friendly cups when they are about 12 to 14 months old, or even earlier, mainly because extended bottle-feeding, especially overnight, is thought to boost the risk of cavities and may contribute to iron deficiency.
Gooze said their findings might provide an added incentive for weaning, and that it may be needed, since many two-year-olds appear to still be using bottles.
Of the 6,750 children studied by Gooze, 1 in 5 was still using a bottle at the age of 24 months, either at night or all the time. And of those long-term bottle users, roughly 1 in 5 was obese at the age of 5.
That compared to about 1 in 6 children who had been weaned earlier.
Gooze and her team then looked at other factors that could affect a child's risk of obesity, including the mother's weight, family income and education, and whether the child had ever been breastfed.
They found that prolonged bottle-feeding by itself was linked to a 33% increase in children's risk of obesity.
"The bottle may be providing a source of comfort, rather than meeting nutritional needs," Gooze said.
The extra calories may be substantial. As an example, Gooze said that if an average-size two-year-old girl drinks an 8-ounce bottle of whole milk at bedtime that would meet 12% of her calorie needs for the day.
Prolonged bottle-feeding may also get in the way of toddlers having a varied, nutritious diet.
The current study shows an association, and not necessarily cause-and-effect, but added that the findings do raise the importance of early life in the risk of childhood obesity.
When did your child stop using the bottle?